Risen From the Shadows
by RagingSceptile
Summary: After being charged for one of the most heinous acts in the League history, Ash & Pikachu are forced to flee when nobody believes that they were set up. Only with them gone nobody knows the truth about how the Shadow Pokemon returned. Except the one who released them. It's not over yet, Ash still wants to get rid of the Shadows but how can he when he's a wanted man? AbilityShipping
1. Prologue

Risen From the Shadows

Prologue

* * *

 **Disclaimer; I don't own Pokemon or any of it's characters.**

 **Okay, so just to start you off this story takes place about three years after where the anime is now, so Ash is about seventeen, almost eighteen now and I'll clear up the other characters ages when they come up.**

 **In addition, this is a different world than we're used to seeing and a lot has happened but everything will be explained eventually, although you'll have to wait until our mysterious hero (note the sarcasm) shows up. And as this is just a prologue, this won't be the length of all the chapters; they'll be a good deal longer.**

 **Without further ado, the prologue….**

* * *

A lone man stood in a dark room. The sunlight from outside doing little to illuminate the pitch black area as the man silently looked out of the large window, not even sparing a glance behind him as the door opened and closed, signifying the entrance of another.

"Sir, it seems the old man is better than we thought. There haven't been any cases of attacks south of Viridian City, we think it's his doing." The man who recently entered the room said. The other man growled.

"No matter, he thinks he can stop me just by keeping in a little safe haven? He better think again. Almost all of Kanto has been overrun with the Shadow Pokemon. It's only a matter of time before all the other regions fall, just like Sinnoh." He told himself.

"Aren't you forgetting that Kalos recently took back Lumiose City? That put us in a really bad place, sir. And our only remaining gateway to Unova is Undella Town." The grunt replied. The other man scowled, still without turning around.

"Unova doesn't matter anyway, we only need them for resources. After we get through Oak's blockade in Viridian, we'll be dominating in this war. And then Team Umbra will be the defining force in the Pokemon World, and not a soul will be able to stop us. Not Professor Oak, not Champion Cynthia, not even Lance of the G-Men!" He bellowed, turning around so his grey hair shined in the flicker of sunlight.

"If I may, Tobias, I wouldn't be so confident if I were you." Another voice said, the door opening once more revealing the old form of Dr. Zager.

"And why not? What would you know about being a leader?" The man, now known as Tobias, answered. Zager glared.

"The one who knows the truth is still out there, running free. You can't rest until he has been eliminated. Then and only then will we be winning this war. Until that happens we're always in danger of falling apart, crumbling down from the pinnacle of power, coming so close to-" Zager ranted until a loud growl cut him off.

"He is a wanted man, Zager. He's been running for three years ever since the incident on Red Rock Isle and I doubt he's going to make a return to civilization anytime soon. Even if he has been silently opposing us from our blind-sides, he is all alone and, after Red Rock, there's no way anyone will side with him even if it's against us." Tobias justified.

"You underestimate that boy, Tobias. The last time you underestimated someone your Darkrai was defeated for the first time. Coincidentally, it's the same person." Zager insisted. "Hell, we thought he was dead after Red Rock. Twice. We all did, but he's proved us wrong too many times to not worry."

"We're the only people that even know he's alive at this point, in case you've forgotten. Everyone else believes him to be dead already, they don't know half as much as they think they do and just because one kid, who has been hiding from civilization for almost four years, is still out there doesn't mean we're doomed." Tobias almost yelled, ignoring Zager's glare. "Now then, I want all the forces in Cerulean to move south and break through whatever defenses the old man has at the end of Viridian. Am I understood, Dr. Zager?"

"Yes, sir." Zager said grudgingly as he left. Tobias vaguely noted the grunt from before wasn't still here and figured he fled when the words between Zager and himself got heated.

'It's for the best,' Tobias though to himself, returning to staring out the window. 'Couldn't have too many people knowing those kinds of things. Imagine the chaos if just anyone knew Ketchum was, in fact, alive.'

* * *

 **Yeah it gets pretty dark but don't worry I won't be going into too much detail about it, you guys and girls can probably fill in most of the blanks yourselves.**

 **Alright, so follow/favorite and don't forget to leave a review because I'm pretty sketchy on how this turned out. I feel like it would do better if I gave a chapter first instead of a prologue but whatever. R &R anyways. And you can probably expect another update by the end of the weekend, so stick with me. Until them, enjoy!**


	2. Chapter 1: Coronet Excursion

Risen From the Shadows

Chapter One: Coronet Excursion

* * *

"Finally, a toast to Professor Oak! We couldn't have held those shadows off at Viridian without you, and I'm sure everyone agrees when I say you've been a tremendous help in keeping the residents of Pallet safe, considering what's been going on." Brock finished, holding his glass of champagne up. He got a round of cheers.

"To Professor Oak!" The room cried, before going back to their own business. Brock smiled a bit to himself as he sat down again.

He didn't quite know what to do with himself at these things. They weren't fancy; everyone wore their day-to-day clothes. He wore nothing to them that he wouldn't at home, which today was a grey vest with an orange t-shirt underneath and grey long pants to match his grey and black sneakers.

Often times when they had a major breakthrough or accomplishment against the Shadow Force, all the residents of Pallet, the second largest stronghold in Kanto, got together to celebrate. Now, he himself wasn't a resident. Or at least, he didn't used to be. He was now, after his hometown of Pewter was burned down in less than a day, but he couldn't quite call it home yet.

Misty was residing there too, actually, even before Cerulean was overrun. She moved in to keep Mrs. Ketchum company after the incident on Red Rock Isle. Actually, many people from Kanto fled to Pallet after the Shadow Force started moving down on Kanto. Especially once they heard how good a job Professor Oak did acting as a general, keeping any and all trespassers from the town.

But she wasn't here right now, Oak had sent her and Tracey on an errand to Vermillion City and they weren't due back until morning. If it were anyone else, Brock would've demanded he go along, he was one of Oak's right hand men, after all, and the trip to Vermillion was no cakewalk. But Misty and Tracey were more than capable of watching out for themselves, let alone when they were together.

Brock sighed, looking out at the party as all the others mingled amongst themselves. He would've demanded to go just for better company if he had known one of these get-togethers would happen.

"Having fun, Brock?" The familiar voice of Professor Oak came from behind, in his signature lab-coat and khaki pants. Brock wheeled around quickly, smiling as big a smile as he could manage to fake.

"You bet, Professor." He lied, although he knew Oak would see right through it. Sure enough, he did.

"You don't need to pretend for me, my boy. Between you and me, I could do without these things too." Oak joked, sitting next to him.

"Really? But you're the guest of honor!" Brock mocked, knowing Oak would suddenly get modest, and nudged his elbow.

"I was just doing what I've always done, Brock, and that's keeping what matters to me safe. You should know by now that nothing bad ever happens when I'm around." Oak said, using Pallet's running joke.

"Makes me wonder why you're still here hanging around with little ol' us instead of being up there in Unova." Brock replied jokingly, only the statement had a hint of honesty in it. He wondered what kept the professor from leaving.

Unova was basically the stronghold for the survivors. It had the least shadow pokemon and was bothered the least by the Shadow Force and served as almost a command center of sorts where many of the big-names resided and remained in charge, such as the champions, professors, Mr. Goodshow and even Scott, not to mention quite a bit of gym leaders and frontier brains.

Of course there were exceptions to every rule. Cynthia and Diantha spent more time in Sinnoh, despite it being thought of as a lost region by now, having made a fort in Veilstone the last Brock heard. Elm and Birch had left Unova together in an attempt to reach Kanto, but they hadn't arrived yet and were laid over in Goldenrod as of now. Sycamore and Juniper both remained as top scientists in Unova, however. And Brock knew of quite a bit of gym leaders that preferred to spend their time outside of Unova, including himself and Misty. And as far as he knew only three of Kanto's Frontier Brains permanently resided in the far away region.

"Phish-posh, Brock. I was born here, and so here is where I will continue to defend. If I was needed for something I wouldn't say no, but until then I will continue to protect my home. Just like you and Misty are doing, you are both definitely capable of making it to Unova and would no doubt be a great help, but you remain here because it's where you grew up." Oak explained, smiling.

"There's another reason, Professor. And I think we all know what it is." Brock said, looking down once more. Oak winced.

"Yes, I believe he is part of my reason as well." Oak said, his voice dropping. "I guess even after all these years I can't forget about him, even after…" Oak trailed off, not daring to speak further. He was stopped by a growl.

"He didn't do it." A new voice said.

Brock and Oak snapped their heads up to see Gary Oak, in a purple shirt, as usual, and blue long pants with blue sneakers, pull out a seat across from them, a hard look on his face. He and Professor Oak had discussed this many times.

"Gary, I know you and he were close and I know it hurts, but all the evidence says that-" Oak started gently once again, but Gary glared.

"Screw the evidence!" He hissed. "What about all the evidence form before, where he saved the world? Or brought down those weirdo's at Team Galactic? Or when he went out of his way to help even strangers? Because that doesn't sound like someone who would blow up an island to me." Gary ranted. Brock knew he had given the same speech many times before.

Gary was one of the few people who had absolutely no doubts in his mind that he was completely innocent. As far as Brock knew there was only a select few people across all the regions that believed that, and the only one still pushing as fiercely as three years ago was Gary.

He and Misty wanted to believe their friend was innocent and there were definitely holes in the case against him, but as far as they knew there was nothing besides his word saying he didn't do anything. Lance and the G-Men had confronted him after and he fled. What innocent person flees? They both hoped there was a good explanation though. Even still.

May was on the rocks with him even before that, since before he went to Kalos. Drew had convinced her he was trying to 'taint her coordinating spirit with that of a league trainer', just like he had done before, which was what made her decide to travel alone to Johto. As such, she had hardly communicated with anybody in their circle besides Dawn, a fellow coordinator, and stopped almost entirely after… the incident.

Dawn, at first, believed there was a good explanation as to what happened, and one that didn't involve him deciding to blow up an island. But after spending time with Kenny, either changed her mind slightly or just decided not to think about it because she never brought up the topic again. Granted it was touchy for everyone, but Dawn completely shut down for hours at a time.

Iris and Cilan, as far as Brock knew, abandoned him immediately. They spoke openly about their distaste for him and vowed how they should've seen it coming. Even though he himself couldn't say he didn't believe it, it made him sick how fast they turned on their supposed 'friend'. Maybe that was why he never liked talking about Unova.

Serena, Bonnie and Clemont were also active in supporting him. They had some doubts over time, but they knew there was no way the kid they had traveled half-way around Kalos with would ever do such things. Right? Active as they were, they weren't more outspoken than Gary Oak.

"Just because he's done good things, doesn't negate bad ones. Red Rock Isle was the start of this whole thing so in essence while he has saved the world in the past it was ultimately he who doomed it." Oak said strongly.

Oak, although he originally fought the claim that he was involved, eventually accepted it as a hard truth. If anything, he resented the boy for starting the whole thing and chickening out and running to Orre, where he was believed to have died only a few hours after fleeing Red Rock Isle.

"No, that was whoever released the shadow pokemon." Gary said, glaring as he got up.

"So, him then?" Oak said back heatedly. Gary only shook his head in disappointment as he retreated back into the crowd. "I'm sorry you had to see that." He apologized to Brock, who waved him off.

"Don't worry, I understand. Family disagreements. Misty has the same problems with her sisters all the time." Brock tried to joke. Oak offered a weak smile.

"Enjoy the rest of your night, Brock." Oak said simply, getting up and walking in the opposite direction as Gary. Brock sighed once more.

"It's killing you, isn't it?" A new voice whispered in Brock's ear. He quickly spun around to meet the owner of the voice, his girlfriend Lucy, from the Battle Pike.

"What is?" Brock asked, moving over as she sat where Oak had previously. She smiled a rare smile.

"The whole debate on whether he's innocent or not in general, but those two disagreeing in particular." She said, sure of herself. "You wish you could be as decisive as them. You still don't know what to think."

"How did you know that?" Brock asked, as if they had just met. She smiled.

"Because I know you, sweetie. You may have never told me, but that doesn't mean I didn't know." Lucy replied.

"But, how?" Brock asked once more, not understanding.

"I guess because I'm in the same position myself." Lucy admitted with a sigh. "It's been three years, and there is still so much controversy. Even if it's dropped, or if nobody speaks up about it anymore the fact it's still a debate is enough. It's so… strange. So out of ordinary. So…" Lucy trailed off, unable to continue.

"So Ash." Brock finished, giving a sad smile.

* * *

"Go for Scott." A fat man in a Hawaiian t-shit said as he picked up the phone.

"Scott? It's Diantha." The Kalos champion's voice sounded strained, and held some kind of urgency to it. He heard a snort in the background.

"Scott, huh? At least we got someone competent on the line." Cynthia's voice rang out next. Her fellow champion ignored her.

"We need an extraction team sent out for us, like, now. We were crossing through Mount Coronet when a horde of shadow pokemon converged on us. Cynthia managed to block them off, but she sealed us in here too. And Garchomp and Gardevoir are too tired to break us out, much less fly us home." Diantha explained, although Scott heard muffled complaints at where all the blame was thrown.

"I'll send a team your way now, and I know just who to send. They're about to be leaving Hoenn for Kalos, shouldn't be too much of a detour." Scott said turning to the map of the world he had open. "Let me give them a ring." He said, putting down his landline in favor of another.

The fat man quickly punched in a series of numbers, praying for a quick answer. Arceus was on his side today. Or Cynthia and Diantha's side, because the 'team' he spoke of was only formed yesterday and their maiden mission was just changed to that of a rescue.

Impromptu, yes, but it was the best he had on such short notice and they were the closest available team.

"Hello?" A sleepy voice answered, which Scott recognized immediately. He'd heard the same one many times.

"Anabel, it's Scott. I have a mission for you." He said smiling. He knew she was rolling her eyes right now.

"Yeah, I know. That's what we were leaving Hoenn for remember? Only we still had another six hours of sleep left." Anabel replied dryly. Scott smirked.

"Not that one, a new one. One that just came in and takes priority over your previous one." Scott said. He took her silence as a sign to continue. "You have to head to Sinnoh before you go to Kalos, on a rescue mission. Champions Cynthia and Diantha are trapped in Mt. Coronet and you three are my closest available team qualified for an extraction mission."

"What the hell were they doing that they need to be rescued at midnight? It's time for sleep not work." Anabel complained, but Scott could hear she was starting to wake up.

"Work never rests, Anabel." Scott told her and suddenly, it felt like they were back at the Battle Tower again.

"And apparently neither do the people that work." She grumbled, but Scott heard and chuckled lightly. "We'll move out soon, Scott. Let me wake up the others." She said finally.

"I knew I could count on you guys. Call in if you need anything and after the mission, I expect details." Scott said, before he hung up the phone.

Next he turned to the map of the world that was being displayed on his computer. He hit a key and instead of being just a blank map, dozens of little markers appeared all across the map in all of the different regions. He changed the course of one from Kalos, to Sinnoh and moved the two female champions pins into Mt. Coronet.

He played around with some of the other pins, giving them an update of sorts, before sighing and looking at one pin that was different from the rest. Instead of matching with most other markers, this one stood out and was the only one in Scott's system that was different.

Red markers were ordinary individuals, while Blue were teams of two or three. Groups of four or more got green markers and G-Men were white while researchers and scientists were tan. Anyone champion level got a purple marker while his own was light blue and floral patterned, which was the only other one that didn't share it's color with another marker.

No, instead this one that was colored bright yellow seemed to clash with his whole system. He looked at it again and let out a small smile, seeing it's estimated vicinity to Mt. Coronet.

Scott let out a sigh. Trying to keep dabs on someone who was supposed to be dead wasn't easy, especially when almost everybody said they were already dead. But he had managed, sort of, using the reports of a strange figure and his knowledge of said figure, if it was the person he thought it was.

At this point, he didn't care how it happened; whether by his team or by this mysterious yellow pin, but he wanted the two champions safe and sound as soon as possible. Until then, he refrained form sighing again and clicking another button, making the pins disappear once more, and turned back to writing in his notebook.

* * *

"ThunderBolt, now." A man, dressed in a navy blue long sleeve shirt and black baggy pants, said calmly.

The Pikachu that stood in front of him complied immediately, leaping into the air and firing off an arc of crackling electricity at the target, which in this case was a shadow Houndoom, who stood no chance at dodging the attack. Instead it tried to break through the electric attack with a Flamethrower, but to no avail. The ThunderBolt quickly obliterated the Flamethrower and struck the Houndoom, causing it to collapse in a heap onto the ground.

"Iron Tail to your left then break into Quick Attack." The next order came.

The Pikachu understood the vague order immediately, powering up a glowing tail and swinging it to it's left which easily swatted away a shadow Wigglytuff before springing forward with Quick Attack and sending the Bulbasaur, which was trying to attack with it's vines, flying back into a rock wall.

"Incoming Stone Edge, block with ElectroBall." The man continued to instruct.

Once more, the Pikachu understood and spun around on the drop of a time. It had already started powering up a sphere of electricity in its tail that continued to grow rapidly. Instead of firing, however, the electric rodent held it's tail before it with the sphere in hand and just as expected, the unfired ElectroBall stopped the Stone Edge in its tracks.

"Good job Pi, that'll show 'em." The man praised. Pikachu let out a smile.

" _We got 'em now, Ash. They're on their last legs and then we're home-free."_ Pikachu replied. Ash smiled back.

"Now, let's finish this." He quickly became serious again. "Agility into Brick Break, make sure that Bulbasaur doesn't get back up. Then continue Agility."

Ignoring the Pokemon that fired the Stone Edge, a large shadow Rhyperior, for now, Pikachu disappeared in a flash and continued to appear and vanish in various places until it was right next to the almost fainted Bulbasaur. Then, Pikachu struck it with its tail before vanishing again, continuing Agility.

"Agility into repeated Iron Tail's." Ash commanded.

The large rock-type stood no change against the onslaught of steel-type attacks even from the tiny mouse. Rhyperior tried to swat him away but Pikachu vanished just in time every time, always striking when Rhyperior was disoriented and with the power-levels this particular Pikachu held, the Rhyperior was quickly dealt with.

Afterwards, Pikachu smoothly landed on the ground and let the glow fade from his tail as he finally lowered his guard and sprinted towards Ash, easily climbing to his rightful place on his best friend's shoulder. Ash chuckled as Pikachu rubbed its cheek on his.

"Yeah, great job buddy. You were awesome." Ash praised, scratching Pikachu's other cheek.

" _As usual."_ Pikachu added happily. _"Now, what are we going to do about the champions that are still trapped in that mountain?"_ He asked next.

"I'm sure they've already signaled for help and it's on the way. Best not to get involved, pal, you know that. We shouldn't be here when they get here, that'll only lead to trouble." Ash replied after some thought. His logical side had won out over his emotional side.

" _I guess that's true. They have plenty of air in there and it's not like they can't afford to wait it out."_ Pikachu said, looking back at the caved in mountain pass.

Just as Ash and Pikachu got ready to walk away from the scene, a large rumble was heard. The duo quickly turned around to see a part of the rock wall getting ready to cave in, as shown by the large cracks in the outer wall that seemed to be expanding as more pressure was put on the space.

"You just had to keep talking, didn't you Pikachu?" Ash sighed out, before sprinting back to the cave wall.

"Is this about where they got stuck?" Ash asked, feeling around. It was hard to tell among the mass of rubble and large boulders.

" _Take a shot in the dark, what's the worst that could happen?"_ Pikachu suggested, hopping down to the floor. Ash sighed with a nod and Pikachu started to hack away with Iron Tail.

Only a few hits later, they heard more rumbling. Ash looked up to see more rocks getting ready to slide down the cliff-side.

"Wait, Pi, stop!" Ash cried, but Pikachu had already sprung once more. One more strike had done it, a hole in the wall was opened and the rocks shook free and started to roll down.

Reacting instantly, Ash sprinted and scooped up his little yellow friend and dove forward, through the opening that little creature had made, narrowly avoiding the avalanche of rocks that fell their way. After a lot of shaking and quaking, the dust settled and Ash stood from his crouched position and Pikachu scurried from his arms to his shoulder.

The teenager sighed as he took a look around, hoping against all odds they weren't stuck in the cave. The fates were not with him today, however, because he quickly saw the hole Pikachu had previously made was now sealed again and they had already learned about what happens when you try and make your own. Needless to say neither of the two were looking for that to happen again.

"That. That's the worst that could happen." Ash huffed out, turning away from the newly created wall to trudge deeper into the cave.

" _No it isn't, we're still alive aren't we? And together. It could've been way worse than this."_ Pikachu argued back. Ash rolled his eyes.

"I guess so." Ash said with a sigh. "Now, how do you suppose we get out of here? And check on them as well, I suppose."

" _Oh so we're saving them now that we have nothing else to do?"_ Pikachu asked rhetorically.

"We're checking on them because they may have been hurt by our little cave-side adventure." Ash corrected.

" _Might as well get them out, then. How can we just walk away when they'll probably ask for help anyways? Besides, maybe we can wait and be rescued too instead of trying to find our own way out."_ Pikachu suggested.

"You know we don't do people, bud. We can't." Ash argued.

" _It's not like we have to stick around or tell them anything, we could be out of there as soon as an opening appears. They won't bother chasing us, not like anyone would think about that when they still have possibly injured champions in a hole."_ Pikachu explained. Ash sighed.

"We'll see how it plays out, Pi. If it really seems to turn out that easy then we'll go for it." He decided. Pikachu nodded his agreement.

" _Can you sense their auras?"_ Ash's starter asked. The trainer paused as he shut his eyes to concentrate better.

"Looks like they're in deeper and another level or so down." Ash said, opening his eyes once more. The two sighed in unison.

"I guess we better head out, we want to be there when help gets here." Ash reasoned, making his way into the cave, Pikachu on his shoulder.

 **So, that's chapter one.**

 **Sorry to end it there, it was going to be longer but the ending would have felt really forced so, again, consider longer chapters in the future. But yeah, this world is a lot different than what it used to be. Three years of shadow pokemon run amuck will do that to a place. And just to clear a few things up…**

 **a) Tobias' team operates almost completely unknown, so not many people know the true name of them hence everybody addressing them as the 'shadow force'**

 **b) The world has become very militarized, and there are very few places and people that haven't anymore**

 **Also, I haven't decided quite on Anabel's team past one other person. It's definitely a three or four person team but Sabrina is the only person I feel inclined to add, so thoughts/suggestions on that would be appreciated.**

 **Thanks for reading, don't forget to review and always ask questions because I will be answering them all**


End file.
